Website Security Black Holes?

I had a real basic website that was repeatedly attacked with virus injections after moving to a new server last year. I finally removed the site from the server to a new server, but the guy at the old server told me to “remove the security black holes in the web code” which I have no idea what that means. We took out everything out of the site except for BASIC html – so it is literally just regular html and jpgs – we even took the paypal pay html out.
Is there any way for me to run some program that checks for “security black holes?” This is a really basic, harmless animal rescue website that has been up for 11 years and started getting attacked this past year and we can’t figure why.

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